Bioinformatics-Driven Structural and Functional Characterization of Caffeine Synthase (CCS1)

Authors

• Asia Khalil, Department of Biotechnology, University of Central Punjab, Lahore, Pakistan
• Muhammad Naveed, Department of Biotechnology, University of Central Punjab, Lahore, Pakistan
• Raja Muhammad Ahmad, Department of Chemistry, Allama Iqbal Open University, Islamabad, Pakistan
• Sania Saeed, Department of Zoology, Virtual University, Islamabad
• Ayesha Hameed, Department of Biotechnology, University of Gujrat, Pakistan
• Ayman Iqbal, Department of Biotechnology, University of Central Punjab, Lahore, Pakistan
• Fakhra Nazir, Capital University of Science and Technology, Islamabad, PakistanFollow

Abstract

Caffeine synthase (CCS1; EC 2.1.1.160) is a S-adenosyl-L-methionine (SAM; S-adenosyl-L-methionine) dependent N-methyltransferase that executes the final methylation steps of caffeine biosynthesis in coffee, tea, and related plants. While paraxanthine can act as an efficient substrate, it contributes to a comparatively minor branch in the overall pathway. We conducted an integrated in silico analysis of CCS1, covering sequence retrieval, structure prediction, 3D modeling, and mutation assessment. Secondary structure was inferred using PSIPRED; physicochemical indices were computed via AA-PROP; 3D models were generated by I-TASSER and evaluated by Verify3D; and missense effects were prioritized using PolyPhen-2, PROVEAN, I-Mutant, and PhD-SNP. Taken together, our results reinforce CCS1’s membership in the methyltransferase superfamily, support a Rossmann-like fold, and highlight residues plausibly linked to substrate preference and structural stability. These findings provide a computational foundation for engineering low-caffeine cultivars and for hypothesis-driven wet-lab experiments on purine alkaloid metabolism.

Article History

Received: Nov 28, 2024; Accepted: Sep 30, 2025; Published: Sep 30, 2026

Recommended Citation

Khalil, A., Naveed, M., Ahmad, R. M., Saeed, S., Hameed, A., Iqbal, A., & Nazir, F. (2026). Bioinformatics-Driven Structural and Functional Characterization of Caffeine Synthase (CCS1), Journal of Bioresource Management, 13 (3).